Fails to install when there is a parent library path and do not recognize parent libsPath

[latot]

Hi, I'm using Ubuntu Noble, and I found pak fails to install when you have packages on /usr/local/lib/R/site-library.

Example:

For root:

sudo bash
R
pak::pkg_install("dplyr")

Now in a normal user:

R
pak::pkg_install("dplyr?source")
                                                                           
→ Will install 1 package.
→ The package (1.21 MB) is cached.
+ dplyr   1.1.4 [bld][cmp]
  
ℹ No downloads are needed, 1 pkg (1.21 MB) is cached
ℹ Building dplyr 1.1.4
✔ Built dplyr 1.1.4 (13s)                                       
Error:                                                            
! error in pak subprocess
Caused by error in `verify_extracted_package(filename, pkg_cache)`:
! /tmp/RtmpNBsw5r/file5b8627a64e601/dplyr_1.1.4_R_x86_64-pc-linux-gnu.tar.gz is not a valid R package, it is an empty archive.
Type .Last.error to see the more details.
> .Last.error
<callr_error/rlib_error_3_0/rlib_error/error>
Error: 
! error in pak subprocess
Caused by error in `verify_extracted_package(filename, pkg_cache)`:
! /tmp/RtmpNBsw5r/file5b8627a64e601/dplyr_1.1.4_R_x86_64-pc-linux-gnu.tar.gz is not a valid R package, it is an empty archive.
---
Backtrace:
1. pak::pkg_install("dplyr?source")
2. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
3. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("pkg_install_do_plan", asNamespace("pak"))(...)
 3. proposal$install()
 4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
 5. base::withCallingHandlers({ …
 6. pkgdepends:::handle_events(state, events)
 7. pkgdepends:::handle_event(state, i)
 8. proc$get_result()
 9. processx:::process_get_result(self, private)
10. private$post_process()
11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
13. base::throw(pkg_error("{.path {filename}} is not a valid R package, it is an empty archive.", …
14. | base::signalCondition(cond)
15. global (function (e) …

This is actually half of the problem, pak should check permissions, and if do not have them, should request to use a local directory.

The second half is if we have a new library pah, we can make a local one just trying to install dplyr normally:

install.packages("dplyr")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages("dplyr") :
  'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘/home/cit_16/R/x86_64-pc-linux-gnu-library/4.4’
to install packages into? (yes/No/cancel) yes
## CANCEL NOW

Now that the local folder exists, we can see the second issue, is that in case we have multiple paths on libPath, pak will ignore all of the others, install a package in root means will store on /usr/local/lib/R/site-library which also has other packages, but if we try to install again:

pak::pkg_install("dplyr")
                                                                          
→ Will install 16 packages.
→ All 16 packages (6.16 MB) are cached.
+ cli          3.6.3  [bld][cmp]
+ dplyr        1.1.4  [bld][cmp]
+ fansi        1.0.6  [bld][cmp]
+ generics     0.1.3  [bld]
+ glue         1.8.0  [bld][cmp]
+ lifecycle    1.0.4  [bld]
+ magrittr     2.0.3  [bld][cmp]
+ pillar       1.10.1 [bld]
+ pkgconfig    2.0.3  [bld]
+ R6           2.5.1  [bld]
+ rlang        1.1.4  [bld][cmp]
+ tibble       3.2.1  [bld][cmp]
+ tidyselect   1.2.1  [bld][cmp]
+ utf8         1.2.4  [bld][cmp]
+ vctrs        0.6.5  [bld][cmp]
+ withr        3.0.2  [bld]
  
ℹ No downloads are needed, 16 pkgs (6.16 MB) are cached
ℹ Building cli 3.6.3
ℹ Building fansi 1.0.6
ℹ Building generics 0.1.3
ℹ Building glue 1.8.0
ℹ Building magrittr 2.0.3
ℹ Building pkgconfig 2.0.3
ℹ Building R6 2.5.1
ℹ Building rlang 1.1.4
^Cstalling...

Pak will reinstall everything, even the packages that are already provided from a parent libPath, is ignoring all the installed libraries.

[1] "/home/cit_16/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/usr/local/lib/R/site-library"                 
[3] "/usr/lib/R/site-library"                       
[4] "/usr/lib/R/library"

Tested on git Pak.

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] processx_3.8.4 compiler_4.4.2 R6_2.5.1       cli_3.6.3      tools_4.4.2   
[6] callr_3.7.6    ps_1.8.1       pak_0.8.0 

Thx!